Protein target profile

VK055_1195

indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase

Genome: KpATCC43816 Gene: AIK79818.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GW36
Length 452
Pocket druggability 0.972
Metabolic reactions 2
Chokepoint Yes
Direct ligand evidence 0 58 total records
Functional annotation 0 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
46.222 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.72 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.972
Structure A0A0H3GW36
Pocket Pocket 1
P2Rank 0.916
Structure A0A0H3GW36
Pocket Pocket 1
ColabFold model
FPocket 0.969 · Pocket 1
P2Rank 0.935 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Phenylalanine, tyrosine and tryptophan biosynthesis, no isoenzyme backup detected, more central than 94.4% of genes in this genome, no human homolog detected.

Relative network centrality 94.4% more central than 94.4% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MQTVLAKIVADKAIWVEARKQQQPLASFQNEIVPTQRNFYDALAGTRTTFILECKKASPSKGLIREDFDPAAIASIYKHYASAISVLCDEKYFQGSFDFLPIVSQVAPQPILCKDFTIDPYQIYLARYYQADACLLMLSVLDDEQYRQLSAVAHSLNMGVLTEVSNEEELERAIALKAKVVGINNRDLRDMSIDLNRTRQLAARLGPDVTVISESGIHTYAEVRELSHFANGFLIGSALMEQADLEAAVKRVLLGENKVCGLTRPQDAQVAWESGAIYGGLIFVPTSPRAVNDAQAKAVIAAAPLQYVGVFRNAPLEEVVARAQALGLAAVQLHGDEDQAYIDALRDALADNVRIWKALSVGETFPARTLRHVDKYLLDNGQGGSGQRFDWSLLQGQDLRNVMLAGGLGADNCVEAAKSGCAGLDFNSGVESQPGIKDASKLASVFQTLRAY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0004425 Catalysis of the reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O.
  • GO:0004640 Catalysis of the reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate.
  • GO:0006568 The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
  • GO:0000162 The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
2 260 PANTHER PTHR22854 TRYPTOPHAN BIOSYNTHESIS PROTEIN
2 260 InterPro IPR045186 Indole-3-glycerol phosphate synthase
257 450 SUPERFAMILY SSF51366 Ribulose-phoshate binding barrel
257 450 InterPro IPR011060 Ribulose-phosphate binding barrel
257 447 Pfam PF00697 N-(5'phosphoribosyl)anthranilate (PRA) isomerase
257 447 InterPro IPR001240 N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain
259 446 Gene3D G3DSA:3.20.20.70 Aldolase class I
259 446 InterPro IPR013785 Aldolase-type TIM barrel
5 251 Pfam PF00218 Indole-3-glycerol phosphate synthase
5 251 InterPro IPR013798 Indole-3-glycerol phosphate synthase domain
50 68 ProSitePatterns PS00614 Indole-3-glycerol phosphate synthase signature.
50 68 InterPro IPR001468 Indole-3-glycerol phosphate synthase, conserved site
257 447 CDD cd00405 PRAI
255 452 Hamap MF_00135 N-(5'-phosphoribosyl)anthranilate isomerase [trpF].
255 452 InterPro IPR001240 N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain
1 258 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 258 InterPro IPR013785 Aldolase-type TIM barrel
259 446 FunFam G3DSA:3.20.20.70:FF:000165 Multifunctional fusion protein
3 254 Hamap MF_00134_B Indole-3-glycerol phosphate synthase [trpC].
3 254 InterPro IPR013798 Indole-3-glycerol phosphate synthase domain
1 251 SUPERFAMILY SSF51366 Ribulose-phoshate binding barrel
1 251 InterPro IPR011060 Ribulose-phosphate binding barrel
39 252 CDD cd00331 IGPS
39 252 InterPro IPR013798 Indole-3-glycerol phosphate synthase domain
1 256 FunFam G3DSA:3.20.20.70:FF:000024 Indole-3-glycerol phosphate synthase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.972
Likely same site as P2Rank 1 1.6 Å 23 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.916
Likely same site as FPocket 1 1.6 Å 23 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.913
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.02
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.005
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GW36
AlphaFold DB full sequence Viewing
ColabFold VK055_1195
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
137 PDB via homolog 351.2 Da · LogP -1.01 · TPSA 176.8 Open detail RCSB PDB
3RG PDB via homolog Detail RCSB PDB
4RG PDB via homolog Detail RCSB PDB
5RG PDB via homolog Detail RCSB PDB
BE2 PDB via homolog Detail RCSB PDB

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
137 RCSB PDB P00909 351.2 Da LogP -1.01 TPSA 176.8 1 viol. ✓ Clean c1ccc(c(c1)C(=O)O)NC[C@H]([C@@H]([C@@H](COP(=O)…
3RG RCSB PDB P9WFX7 195.2 Da LogP 0.88 TPSA 86.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)NCC(=O)O
4RG RCSB PDB P9WFX7 228.2 Da LogP 2.96 TPSA 46.5 ✓ Ro5 ✓ Clean c1ccc(cc1)OCc2cccc(c2)C(=O)O
5RG RCSB PDB P9WFX7 155.1 Da LogP 1.11 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(c(cc1F)C(=O)O)N
BE2 RCSB PDB P9WFX7 137.1 Da LogP 0.97 TPSA 63.3 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)N
BTB RCSB PDB P9WFX7 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
IGP RCSB PDB P9WFX7 287.2 Da LogP 0.67 TPSA 123.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)[C@@H]([C@@H](COP(=O)(O)O)O…
MLI RCSB PDB P9WFX7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.